Yui and Kirito were teleported somewhere atop the World Tree, where Yui detected Asuna. Yui, in her normal form, did not have access to any mapping data of the World Tree, but knew where Asuna was and guided Kirito through the corridors and exited to the branches. Kirito discovered that there was no City in the sky as claimed, thus the Grand Quest was a complete lie, and cursed Sugou Nobuyuki. They continue running until they see the cage in which Asuna was held prisoner.

Kirito, Asuna and Yui reunited.

Yui destroyed cage's opening and ran in to hug Asuna. Kirito soon joined them and they were happy that they were reunited. Kirito asked Yui if she could log Asuna out, but she sadly replied that Asuna was locked down by complicated codes that required a system console to remove. Suddenly, Kirito turned around as he had sensed something, but the space in the cage distorted into a black space and Yui told them to be careful as something bad was approaching before she disappeared. Kirito and Asuna were forced onto the floor, where they could not move. The so-called Fairy King Oberon then appeared, whom Kirito easily recognized as Nobuyuki. Oberon then kicked Kirito to the ground and stated they were being restrained by gravity magic that would be implemented in the next patch, though Oberon defined it to be somewhat overpowered. Oberon then revealed to Kirito his true intentions behind the game: ALfheim Online was a testing ground for developing technology for controlling human thoughts and emotions. As Kirito and Asuna swore that they would bring down Oberon, the madman stated that they could not stop him for he was a god in ALO.

Asuna chained by Oberon.

Oberon then summoned a pair of chains and attached them to Asuna, after which she was lifted by the chains and left standing only on her toes. Oberon then taunted both of them, stating how NPC women could not replicate such a scared face and then sniffed Asuna's hair and told them how hard it was to replicate her scent from the real world. Kirito ordered Oberon to stop while trying to stand up, but Oberon kicked him and stabbed him with his sword. Shortly afterwards, Oberon used a system command to reduce the Pain Absorption level from 10 to 8 to make Kirito start feeling pain from being stabbed. He also said that he would gradually decrease the level and at level 3 or lower, it would affect his physical body in the real world.

Oberon then returned to Asuna and forcefully pulled off her top, then taunted them even more by stating he planned to molest her body in the real world while watching a recording of him doing it in ALfheim, and began to lick her face. Kirito cursed Oberon and swore he would kill him. Feeling helpless, Kirito mourned whether that was his punishment for thinking that he was the strongest game player and for believing that he had the ability to overcome the system. At that moment, Kayaba Akihiko appeared and asked him whether he gave into the power of the system. As Kirito affirmed this, stating that he was nothing more than a player and Oberon was a GM, Kayaba told Kirito that if he thought like that, their battle was a lie. He also told him that he himself had learned from their battle that the human will was more powerful than the system, and then encouraged him to stand up.

Kirito activates Kayaba's system ID "Heathcliff".

As Oberon continued molesting Asuna and began to lift up her skirt, Kirito finally managed to stand up and the sword impaled in his back slid out. As Oberon attempted to slap him to get him back on the ground, Kirito caught his hand and activated Kayaba's system ID, Heathcliff, via a voice command and then revoked Oberon's administrator status. Oberon arrogantly declared ALO as his own, but Kirito remarked that Oberon stole it. The so-called Fairy King then cursed Kirito and tried to generate an Excaliber, but nothing happened and he ended up cursing the system. Instead, Kirito repeated the same command and spawned an Excaliber, which he simply gave to Oberon and grabbed his own sword. He then reduced the Pain Absorption level to zero, causing Oberon to panic, and challenged him to a duel and told him not to run, as Kayaba never did so. This enraged Oberon after he figured out that Kayaba was the one who had helped Kirito, and cursed his rival and randomly swung his sword. Kirito told him that he felt the same when he lost his duel to Kayaba and had to work for him, yet he never wished to be like him.

Kirito delivering the finishing blow to Oberon.

Oberon desperately attacked Kirito, but due to Oberon's lack of combat experience, Kirito easily parried his feeble attacks, then slashed his cheek and Oberon trembled from the pain inflicted on him. Kirito then cut his right arm off, then his legs, and grabbed Oberon's head, shortly afterwards throwing it into the air and then stabbing his right eye with the sword, killing Oberon.

Kirito turned back to Asuna, broke the chains then hugged her and began to cry. Asuna told him that he was her hero, but Kirito admitted that he was actually weak and told her that he would do his best to become stronger. She leaned on his chest and shed a tear as she told Kirito they should do all sorts of things in the real world before he logged her out. Kirito then called Kayaba, as he knew he was there, who then told Kirito that he was Kayaba Akihiko's afterimage. Kirito then thanked Kayaba, but the latter rejected it, stating that they were not close enough to do things for each other for free and that there was a price for his aid.

Kirito receives "The Seed".

Kayaba then gave Kirito an object called World Seed that was the beginning of a world and told him that he wished to see it grow, although it was up to Kirito's choice on what to do with it. Kayaba then left, hoping the two would meet again. In a yellow binding light, Kirito was warped back to the birdcage. He then called for Yui, who popped out from nowhere and hugged her "papa", stating she hid in Kirito's NerveGear's memory. He informed her that Asuna had returned to the real world, and Yui felt a little disappointed for her not being with them, but he stated that she would come back to the game, to her delight. Yui told Kirito that when Oberon appeared, she hid in Kirito's NerveGear, where Kirito had saved her core programming. Kirito then told Yui that he was about to log out so he could go to the hospital where Asuna was being taken care of. Before logging out, he kissed Yui in the cheek.

Kazuto heading to towards Asuna's hospital.

When Kazuto opened his eyes, he found Suguha waiting and worried as he had been in ALO for a long time. Kazuto informed her that everything was over and thanked her. As she leaned on his chest and he placed an arm around her, Kazuto also informed Suguha that he had rescued Asuna, but as he tried to apologize, Suguha immediately told him to get going to the hospital as Asuna must be waiting for him. Outside where it had begun snowing, Kazuto took his bike and started riding his way to the hospital, with Suguha requesting him to properly introduce her to Asuna.